SIFTS Mapping

SIFTS (Structure integration with function, taxonomy and sequences) provides an up-to-date resource for residue-level mapping between Uniprot and PDB entries. The information is updated and released weekly simultaneously with the release of new PDB entries. SIFTS Entries are published as XML files and made publicly available via an FTP site hosted at the European Bioinformatics Institute.

At the point of viewing a PDB structure, Jalview downloads a SIFTS file for the target entry and uses it to accurately map the sequence residues with the structure residue. Prior to SIFTS integration, Jalview uses Needleman and Wunsch Alignment algorithm to map sequence residues to structure residues, and that may not always result to a correct mapping since it is computational determined.

The default method for 'Sequence ↔ Structure' mapping can be configured in the Structure tab in the Tools → Preferences dialog box. When 'SIFTS' is enabled as the default, all mappings between 'Sequence ↔ Structure' is performed via SIFTS provided that there is a valid SIFTS entry for PDB structure. If no valid SIFTS resource is available, then the 'Sequence ↔ Structure' mapping falls back to Needleman and Wunsch Alignment algorithm.

To verify the mapping method used, you can view the mapping output via the structure viewer menu File → View mapping. A sample mapping output can be seen in the screenshot below. The highlighted position shows the method used.

SIFTS Mapping integration was added in Jalview 2.9.1